Virus classification for viral genomic fragments using PhaGCN2

Viruses are the most ubiquitous and diverse entities in the biome. Due to
the rapid growth of newly identified viruses, there is an urgent need for
accurate and comprehensive virus classification, particularly for novel
viruses. Here, we present PhaGCN2, which can rapidly classify the taxonomy
of viral sequences at family level and supports the visualization of the
associations of all families. We evaluate the performance of PhaGCN2 and
compare it with the state-of-the-art virus classification tools, such as
vConTACT2, CAT, and VPF-Class, using the widely accepted metrics. The
results show that PhaGCN2 largely improves the precision and recall of
virus classification, increases the number of classifiable virus sequences
in the Global Ocean Virome dataset (v2.0) by 4 times, and classifies more
than 90% of the Gut Phage Database. PhaGCN2 makes it possible to conduct
high-throughput and automatic expansion of the database of the
International Committee on Taxonomy of Viruses.